Introduce of microbiology: Part 2

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(BQ) Continued part 1, part 2 of the document Introduce of microbiology has contents: Meet the prokaryotes, say hello to the eukaryotes, examining the vastness of viruses, fighting microbial diseases, teasing apart communities, synthesizing life, ten great uses for microbes,.... and other contents. Invite you to refer.

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Nội dung Text: Introduce of microbiology: Part 2

4 Meeting the Microbes
IN THIS PART . . . Get acquainted with microorganisms from the three domains of life — from those we know a lot about (like bacteria, viruses, fungi, and protists) to those we know much less about (like the archaea and sub-viral particles). Get friendly with the many kinds of bacteria, whether they’re important for geochemical cycles or human health. Get an overview of eukaryotic microorganisms including the yeasts, fungi, and the great diversity of protists that include the algae, the phytoplankton, and the amoeba, among others. Discover the structures and behaviors of the viruses, including those that infect plants, animals, and bacteria.
IN THIS CHAPTER »» Becoming familiar with the Bacteria »» Introducing the Archaea Chapter 12 Meet the Prokaryotes A long with viruses, the prokaryotes make up most of the evolutionary diversity on the planet. A rough estimate puts the number of bacterial and archaeal cells on earth at around 2.5 × 1030. The number of species is harder to pin down. Some scientists think that there are far more prokaryotic species than all eukaryotic organisms combined, whereas others think that it’s the reverse. Either way, more prokaryotic species are being discovered every year, and it’s likely that we’ve just hit the tip of the diversity iceberg! Prokaryote is sort of a misnomer because it’s used to talk about all non-nucleated cells, as opposed to eukaryotes, which have a nucleus and organelles, among other things. Both the Bacteria and the Archaea fall into this category, but they’re more distantly related to one another than are the Archaea and the Eukaryota (the third major domain of life) and so they technically shouldn’t be grouped together. Because the Bacteria and the Archaea have many other similarities, it’s simply more convenient to consider them at the same time in this book. However, archaea and bacteria are fundamentally different from one another in terms of cellular structures and genes, including those used to determine ancestry. Making sense of the vast numbers of different species and lifestyles is no easy task. In truth, scientists will be working for many years and there still won’t be a tidy sorted list. With this in mind, we’ve put together a chapter describing the major differences between the different prokaryotes based roughly on how they’re related to one another and how they live. CHAPTER 12 Meet the Prokaryotes 177
Another term for how things are related to one another in the evolutionary sense is phylogeny. Phylogeny is measured by comparing the genetic code in each organ- ism. There are several ways to do this, which are summarized in Chapter 11. There are three domains of life: Bacteria, Archaea, and Eukarya, and within each are several phyla. A phylum is a major evolutionary division that is then divided again as class, then order, then family, then genus, then species. This type of organi- zation is called taxonomic classification and each of these divisions is called a taxo- nomic rank. Kingdom used to be the highest taxonomic rank until recently when the higher rank of domain was added. Kingdom is still an important rank when describing major groups within the domain Eukarya, but it’s less useful for describing the Bacteria and the Archaea domains. For this reason, kingdom isn’t used in this chapter. Getting to Know the Bacteria Of the two domains of prokaryotes, the Bacteria are the best studied and contain all known prokaryotic pathogens. In reality, only about 1 percent of all bacteria have been studied in any detail and of these only a small proportion cause disease. Some, like Pseudomonas, take the opportunity to colonize humans when their immune system is down, but they aren’t primarily human pathogens thriving mainly as free-living bacteria in soils. Others, like Wolbachia and Mycoplasma, lack a cell wall and cannot live outside a host cell. Figure 12-1 shows a general view of the known phyla in the domain Bacteria. The Gram-negative bacteria: Proteobacteria This phylum contains all kinds of interesting metabolic diversity that doesn’t match the evolutionary paths of diversity. This might be because members have been swapping DNA and have taken on traits that other bacteria had to evolve. This type of genetic transfer is called lateral gene transfer (LGT, or sometimes horizontal gene transfer, HGT) and makes deciphering bacterial evolution a bit tricky. The Proteobacteria can be divided genetically into five major classes named for letters of the Greek alphabet: alpha (α), beta (β), delta (δ), gamma (γ), and epsilon (ε). 178 PART 4 Meeting the Microbes
FIGURE 12-1: The phylogenetic tree of the bacteria. This group seems to have the largest number of species, and many of them have been isolated in laboratory culture. Many members of the Proteobacteria are mod- els for the study of microbial systems like genetics (E. coli) and anoxic photo synthesis (purple sulfur bacteria). Autotrophic lifestyles Nitrifiers oxidize inorganic nitrogen compounds like ammonia and nitrate for energy. All are environmental, found in sewage treatment plants as well as soil and water. They’re different in that they have internal membranes that help with compartmentalizing toxic compounds made as a part of the oxidation process. Ammonia oxidizers have names that start with Nitroso– (for example, Nitrosomonas), and nitrate oxidizers have names that start with Nitro– (for example, Nitrobacter). Sulfur oxidizers live either in acidic or neutral environments rich in sulfur com- pounds. The acid-tolerant sulfur oxidizers (like Thiobacillus) acidify their environ- ment by making sulfuric acid as a waste product during metabolism, and many can also use iron as an energy source. Neutral sulfur environments like sulfur springs and decomposing matter in lake sediments are home to sulfur oxidizers like Beggiatoa that grow in long chains and often have sulfur granules deposited within their cells. On the other side of the coin, sulfate and sulfur can be used by sulfate and sulfur- reducing bacteria. These include members like Desulfobacter, Desulfovibrio, and CHAPTER 12 Meet the Prokaryotes 179
Desulfomonas, all of which are members of the Deltaproteobacteria and most of which are strictly anaerobic — there are some exceptions. If iron is present in the media, these bacteria will cause it to turn black. Hydrogen oxidizers like Paracoccus oxidize H2 in the presence of oxygen (O2), which results in electrons and H2O. They use an enzyme called hydrogenase to produce ATP from the oxidation of H2 (see Chapter 9). Methane is a major gas in places lacking oxygen like the rumen of herbivores or the mud at the bottom of lakes. Here methane is produced by species of archaea that is converted by methanotrophic bacteria, such as Methylococcaceae, back into carbon dioxide or organic material. Nitrogen fixers are actually heterotrophs that fix nitrogen, which is very cool. Very few bacteria are able to fix nitrogen (N2) from the air into a form that is usable in the cell (ammonia, NH4). Those that can are interesting because they need oxygen for their metabolism. Nitrogenase, the critical enzyme for nitrogen fixation, is extremely oxygen sensitive. The nitrogen-fixing bacteria get around this problem in two ways. Free-living nitrogen fixers form a thick slime around their cells that lets them have just the right amount of oxygen but not too much. Others, like Rhi- zobium, live in an intimate association with the roots of plants (such as soybean) inside which they aren’t exposed to too much oxygen. Heterotrophic lifestyles The pseudomonads are ecologically important in soil and water and can break down things like pesticides. They can only metabolize compounds through respi- ration (they can’t use fermentation), but most of the group can do this both aero- bically and anaerobically. They can metabolize many organic compounds (more than 100) but don’t make hydrolytic enzymes, which means that they can’t break down complex food sources like starch. Members of the group include Burkholde- ria, Ralstonia, and Pseudomonas. Several pseudomonad species are opportunistic human pathogens and specific plant pathogens. The genera Neisseria, Moraxella, Kingella, and Acinetobacter are all aerobic, non- swimming Proteobacteria with a similar shape, so they’re often grouped together. The interesting thing about their cell shapes is that many (all except Neisseria, which has a round shape called coccoid all the time) are rod shaped during log growth and then switch to a coccoid shape in stationary phase. Moraxella and Aci- netobacter use twitching motion (see Chapter 4) to get around. Most are found as commensals associated with moist surfaces in animals (such as mucous mem- branes), but some species of each are human pathogens and Acinetobacter in par- ticular is more common in soil and water. 180 PART 4 Meeting the Microbes
The enteric bacteria are facultative aerobes (not inhibited by oxygen) that ferment sugars with many different waste products. The bacteria in this group are all closely related within the Gammaproteobacteria and so are sometimes difficult to tell apart. Many are of medical and industrial importance. Most are rod shaped, and some have flagella, but for the most part they’re distinguished from the pseu- domonads based on the fact that they produce gas from glucose and don’t have specific proteins needed to make the electron transport chain (cytochrome c) needed for respiration. This group includes the following genera: Salmonella, Shi- gella, Proteus, Enterobacter, Klebsiella, Serratia, Yersinia, and Escherichia. Of note is the genera Escherichia that includes the best-studied species of bacteria, E. coli, which has been used in countless research and industrial applications. The genus Yer- sinia contains the species Y. pestis that was responsible for the plague of the Middle Ages. A group of Proteobacteria similar to the enteric bacteria are the Vibrio bacteria. Members of this group do have a cytochrome c gene, but otherwise they’re pretty similar in other respects to the enterics. The group is named for the genus Vibrio, which contains not only the pathogen V. cholera but many other aquatic bacteria that produce fluorescent light in a process called bioluminescence. Other mem- bers of this group include the genera Legionella and Coxiella. The Epsilonproteobacteria include bacteria found as commensals and pathogens of animals like Campylobacter and Helicobacter that are also common in environ- mental samples from sulfur-rich hydrothermal vents. Interesting shapes and lifecycles The Spirillia are spiral-shaped cells with flagella for moving around. They’re dif- ferent from the Spirochaetes, which are distantly related and have different cellular structures. Two interesting examples of spiral-shaped Proteobacteria include Magnetospirillum, which have a magnet inside each cell (see the example in Figure 12-2) that helps them point north or south, and Bdellovibrio, which attacks and divides inside another bacterial cell. A sheath is like a tube inside which many bacterial cells divide and grow protected from the outside environment. Sheathed bacteria are often found in aquatic envi- ronments rich in organic matter like polluted streams or sewage treatment plants. When food gets scarce, the bacteria all swim out to look for a better place to live, leaving behind the empty sheath. Some bacteria, such as Caulobacter, form stalks that they use to attach themselves to surfaces in flowing water. Budding bacteria, such as Hyphomicrobium, reproduce by first forming a long hyphae at the end of which forms a new cell in a process called budding. CHAPTER 12 Meet the Prokaryotes 181
FIGURE 12-2: Magnetic bacteria. Budding is different from binary fission (where the cell divides into two equal parts) because the cell doesn’t have to make all the cell structure before it starts to divide. Budding is often used by bacteria with extensive internal structures that would be difficult to double inside of one cell. The Rickettsias are obligate intracellular parasites of many different eukaryotic organisms, including animals and insects. The Myxobacteria have the most complex lifestyle of all bacteria that involves bac- terial communication, gliding movement, and a multicellular life stage called a fruiting body. When the food sources are exhausted in one site, myxobacterial cells swarm toward a central point where they come together and form a complex structure called a fruiting body that produces mixospores. These mixospores can then disperse to a new location where a new food source can be found. More Gram-negative bacteria Many of the known Gram-negative bacteria are from the phylum Proteobacteria, but there are several other phyla that are also Gram-negative. Each is unique and an important part of the microbial world: 182 PART 4 Meeting the Microbes
WHO’S YOUR DADDY? WOLBACHIA! Species of Wolbachia live inside the cells of their host and infect countless species of beetle, fly, mosquito, moth, and worm (among many others) — more than 1 million spe- cies in all. In some cases, it’s a parasite, causing its host harm; in other cases, it forms a mutualistic relationship with its insect host, a situation that is beneficial for both parties. Some species of insect actually need to be infected with Wolbachia in order to repro- duce successfully. In many cases, infection alters how or if the embryos develop. Here’s an example: The Wolbachia bacteria can infect female eggs but not the male sperm. Infected females then produce female offspring without being fertilized. Infection makes the male sterile so that he can’t fertilize an uninfected female. Other strategies to increase the number of infected female offspring include killing male embryos and changing males into females after they’ve developed. Some of the insects that these bacteria infect are themselves parasites of animals. For example, heartworm that infects dogs requires a Wolbachia infection to reproduce; if the worm is treated with antibiotics, it dies. As we talk about in Chapter 15, however, using antibiotics this way eventually leads to antibiotic resistance in bacteria, so ideally it won’t catch on as a treatment. We still don’t understand a lot about this phenomenon, but research into how it works and how it affects insect, animal, and plant populations is ongoing. »» Cyanobacteria: The phylum Cyanobacteria were likely the first oxygen- making organisms (through photosynthesis) on earth and were critical for converting the earth’s atmosphere into the pleasantly aerobic one it is today. They come in all shapes and sizes, as shown in Figure 12-3, from single cells to colonies and chains with specialized structures where nitrogen fixation occurs (called heterocysts). »» Purple sulfur bacteria: The purple sulfur bacteria use hydrogen sulfide (H S) 2 as an electron donor to reduce carbon dioxide (CO2) and are found in anoxic (oxygen-free) waters that are well lit by sunlight and in sulfur springs. This group contains more than 40 genera with examples such as Lamprocystis roseoper- sicina and Amoebobacter purpureus, as well many species of Chromatium. »» Purple nonsulfur bacteria: The purple nonsulfur bacteria can live in the presence and absence of oxygen in places with lower concentrations of hydrogen sulfide. They’re photoheterotrophs, meaning that they can use photosynthesis for energy but use organic compounds as carbon sources. Many have Rhodo– in their names like Rhodospirillium, Rhodovibrio, and Rhodoferax, among others. CHAPTER 12 Meet the Prokaryotes 183
FIGURE 12-3: Cyanobacteria. »» Chlorobi: The phylum Chlorobi are called the green sulfur bacteria and are also phototropic (gathering energy from light), but they’re very different from the green Cyanobacteria. For one thing, they live deep in lakes where they use hydrogen sulfide (H2S) as an electron donor and make sulfur (S0) that they deposit outside their cells. For another, they don’t produce oxygen during photosynthesis, so they didn’t contribute to the oxygenation of the earth’s atmosphere like the Cyanobacteria did. »» Chloroflexi: The phylum Chloroflexi is also known as the green nonsulfur bacteria. These bacteria are found near hot springs in huge communities of different bacteria called microbial mats (see Chapter 11), where they use photosynthesis to gather energy without producing oxygen. »» Chlamydia: The phylum Chlamydia is made up entirely of obligate intracellu- lar pathogens. These bacteria can’t live outside a host cell, so they must continuously infect a host. Members of this group cause a myriad of human and other animal diseases and are transmitted both sexually and through the air where they invade the respiratory system. »» Bacteroidetes: The phylum Bacteroidetes contains bacteria common in many environments, including soil, water, and animal tissues. The genus Bacteroides can be dominant members of the large intestine of humans and other animals and are characterized by being anaerobic and producing a type of membrane made of sphingolipids that are common in animal cells but rare in bacterial cells. Other important genera include Prevotella, which are found in the human mouth, and Cytophaga and Flavobacterium, found in soils around plant roots. »» Planktomycetes: Members of the phylum Planktomycetes stretch the concept of prokaryote because they have extensive cell compartmentaliza- tion, (see Figure 12-4), usually only seen in eukaryotic cells. These compart- ments are especially useful to keep by-products like hydrazine (a component of jet fuel) contained (see Chapter 9). These bacteria live mainly in aquatic environments like rivers, streams, and lakes where some attach to surfaces by a stalk so that they can take up more nutrients from the surrounding water. These stalked bacteria divide by budding to produce a swimmer cell that takes off to find a new place to attach. 184 PART 4 Meeting the Microbes
FIGURE 12-4: Anammox bacteria. »» Fusobacteria: The phylum Fusobacteria contains bacteria with cells that are long and slender with pointed ends. Some of the species of this group are found in the plaque of teeth as well as in the gastrointestinal tract of animals. They are anaerobic and members include Fusobacteria and Leptotrichia. »» Verrucomicrobia: The phylum Verrucomicrobia are named the warty (from the Greek verru) cells not because they cause warts but because some members look warty. The group is widespread in water and soil, but one Genus in particular is associated with the mucosal membranes of humans. Akkermansia mucilagina is more often associated with the guts of lean people. »» Spirochaetes: The Spirochaetes are highly coiled bacteria common in aquatic environments and associated with hosts. The latter group includes human pathogens such as Treponema pallidum that cause syphilis, species of Borellia that cause Lyme disease, as well those that help to break down wood in the guts of termites. »» Deinococci: The Deinococci share many structures with the Gram-negative bacteria, but because they have a very thick cell wall they stain Gram- positively. Members of this group are so tough that they can withstand levels of radiation 1,500 times higher than would kill a person. Not only do they have a tough cell wall, but they have many different DNA repair enzymes that can take a complete Deinociccus radiodurans chromosome that has been shat- tered into hundreds of pieces by radiation, and put it all back together in the right order. »» Thermotolerant bacteria: Several bacterial groups spanning many different phyla are thermotolerant. Some examples include • Aquifex, which are the most thermotolerant bacteria known. • Thermotoga, which makes a sheath (hence, toga in the name) and contains genes similar to those in the Archaea. CHAPTER 12 Meet the Prokaryotes 185
• Thermodesulfobacterium, which is a sulfate reducer and makes lipids similar to those in the Archaea. • Thermus, that contains, most famously, the species Thermus aquaticus, from which Taq DNA polymerase was isolated. This enzyme is essential to many molecular biology applications because it drives the polymerase chain reaction (see Chapter 16). The Gram-positive bacteria Two phyla, the Firmicutes and Actinobacteria, contain the Gram-positive bacte- ria. Although they both have Gram-positive cell walls, they differ in the propor- tion of Gs (for guanine) and Cs (for cytosine) in their DNA. The Firmicutes are also known as the low G + C Gram-positive bacteria (with between 25 percent and 50 percent G + C), and Actinobacteria are also known as the high G + C Gram- positive bacteria (with between 50 percent and 70 percent G + C). Low G + C: Firmicutes The Firmicutes can be split roughly based on their ability or lack of the ability to form endospores. Dividing the group this way is mainly for convenience because it’s easy to tell endospore formers from nonendospore formers by heating a cul- ture up to kill everything but the spores. Within the two groups, there is quite a bit of phylogenetic and metabolic diversity. Endospore formers, including species of Clostridium and Bacillus, live mostly in soil where endospore formation comes in handy when it’s dry. Some infect animals and cause nasty diseases, but for the most part this is accidental. One important member of this group is Bacillus thuringiensis (Bt), which makes an endospore that contains a crystalline toxin called the Bt toxin (see Figure 12-5), which is partic- ularly effective against many species of insect. Bt toxin is used extensively as an insecticide in agriculture (see Chapter 16). The bacterial genera that don’t form endospores can be grouped further into the Staphylococci and the Lactococci. Both groups contain commensal and pathogenic bacteria of animals and are distinguished by where they’re found and their metab- olism. For instance, the Staphylococci are tolerant of salt and are found on the skin, whereas the Lactococci are fermentative bacteria (Peptostreptococcus and Streptococ- cus), found in the guts of animals (Enterococcus) and in milk (Lactococcus). 186 PART 4 Meeting the Microbes
FIGURE 12-5: Bacillus thuringi- ensis endospore with toxin crystal. High G + C: Actinobacteria The phylum Actinobacteria contains many very common soil bacteria and several bacteria that are commensal of the human body, as well as a few notable human pathogens such as Mycobacterium tuberculosis and Corynebacterium diphtheria. Here are three important genera represented in this phylum: »» Members of the genus Proprionibacterium ferment sugars into propionic acid and CO2 gas and are the main bacteria used to make Swiss cheese. The gas makes the holes in the cheese, and the acid gives it a nutty flavor. »» Colonies of Mycobacteria have a waxy surface because of special acids in their cell walls called mycolic acids that make them difficult to stain in the regular way. Instead, heat and acid are used to stain cells red so that they can be visualized under a microscope. This group has many non-pathogenic mem- bers as well as M. tuberculosis. »» The Streptomyces were thought for a long time to be a type of fungus because they make big filamentous clusters. They are, in fact, bacteria that, instead of dividing by binary fission into individual cells, form mycelia that make spores, which then pop off to populate new areas (see Figure 12-6). More than 500 different antibiotics have been isolated from this group, many of which are used in medicine today. CHAPTER 12 Meet the Prokaryotes 187
FIGURE 12-6: Streptomyces spore formation. Acquainting Yourself with the Archaea Also known as archaebacteria (archaea, from the Greek, means “ancient”), the archaea are thought to be the oldest forms of cellular life on earth. They differ from the bacteria in a few fundamental ways but until recently were thought to be part of the domain Bacteria. When sequencing genes to test the evolutionary rela- tionship between microorganisms became popular, it became clear that the Archaea weren’t part of the Bacteria at all but made up a division of their own. Since their discovery in the late 1970s, there has been a steady increase in the number of described members. Each time a new group is found, information is added to what is known about the evolution of the entire group, because new members help to resolve the branching in the phylogenetic tree, shown in Figure 12-7. It’s likely that many more archaea will be discovered and that the current tree will change quite a bit. Currently, there are two main phyla in the domain Archaea: the Euryarchaeota and the Crenarchaeota. However, within the Crenarchaeota, there may soon be a few new phyla, including the Thaumarchaeota, the Korarchaeota, and the Aigarchaeota. As new archaeal strains are discovered, the gaps in what we know about how all archaea are related get filled in. 188 PART 4 Meeting the Microbes
FIGURE 12-7: The phylogenetic tree of Archaea. As with the Bacteria, there are far too many archaeal species to describe them all here but you can go to www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax. cgi?id=2157 for a complete list. In this section, we discuss representatives of the different forms of archaeal life, filling you in on their ability to tolerate extremes of temperature, acidity, and salinity. It’s likely that the most extreme of the Archaea were some of the first life forms on earth, evolving during a time when the earth was hotter and harsher than it is now. How they’re able to thrive in extreme conditions is covered in Chapter 11. WHERE DO MY GENES COME FROM? The Archaea are interesting because they have many genes that resemble those in bacteria and others that resemble the genes in eukaryotes. This is part of the reason why they confounded microbiologists for years — they couldn’t squarely be placed within the domain of Bacteria or Eukarya. A great example of this is an archaeon (singular for archaea) called Methanocaldococcus jannaschii, which has core metabolic genes that bear some resemblance to those in bac- teria, but most of the genes for molecular processes (things like RNA transcription and protein translation) have similarities to those in eukaryotes. More than a third of its genome (40 percent) contains genes that don’t resemble those in either bacteria or eukaryotes. Archaea likely evolved around the same time as the earliest bacteria. It’s even possible that eukaryotes came from an early archaeal ancestor. It’s mysteries like this that make the microbiology of the archaea so fascinating. CHAPTER 12 Meet the Prokaryotes 189
Some like it scalding: Extreme thermophiles Archaea are well suited to hot temperatures. This is likely because they evolved when the earth was younger and hotter and a much harsher environment than it is now. The most heat-tolerant microorganisms on earth are archaea, and there are many examples that require hot temperatures to grow. Many archaea can not only grow at hot temperatures but withstand even hotter temperatures. In this section, we provide a list of a few of the most extreme and the temperatures at which they can live and grow. A thermophile is an organism that loves heat and grows best at temperatures between 50°C and 60°C but can survive up to 70°C. Hyper-thermophiles (extreme thermophiles) grow best around 80°C to 90°C but can survive in much higher temperatures. Some hyper-thermophiles have been found to survive above 120°C in the high-pressure environment of the deep sea near hydrothermal vents. The following archaea are thermophiles and extreme thermophiles: »» Thermococcus and Pyrococcus are strict anaerobes that get energy from metabolizing organic matter in many different thermal environments. Thermococcus grows fine in a range of temperatures between 55°C and 95°C, and Pyrococcus grows best at 100°C. »» Methanopyrus is a hyperthermophilic methanogen (it produces methane). This group contains a unique kind of cellular membrane not found in any other organism. One species of this group, M. kandleri, is the current record holder for growth at the hottest temperature, at 122°C. Water can attain temperatures this high only in deep ocean environments where great pressure stops water coming out of hydrothermal vents from boiling. »» Nanoarchaeum are very small in size and, as shown in Figure 12-8, live as parasites on another hypothermophilic archaea, Ignicoccus. These two archaea can be found together in hydrothermal vents and hot springs at temperatures between 70°C and 98°C. »» Ferroglobus can oxidize iron anaerobically. It’s likely that Ferroglobus and others like it were oxidizing iron before the earth’s atmosphere contained oxygen, creating blankets of iron deposits on the ocean floor. As time went on, this layer of iron got trapped and is now seen as banding patterns in ancient rocks. »» Sulfolobus lives in sulfur-rich, acidic environments like those around hot springs where it attaches to sulfur crystals oxidizing the elemental sulfur for energy (see Figure 12-9). 190 PART 4 Meeting the Microbes
»» Desulfurococcus and Pyrodictium are strictly anaerobic sulfur-reducing archaea that thrive around marine hydrothermal vents. Desulfurococcus grows best at 85°C, whereas Pyrodictium grows best at 105°C. FIGURE 12-8: The parasitic Nanoarchaeum living on the cells of Ignicoccus. FIGURE 12-9: Sulfur crystals covered in the Sulfolobus (left) and a closeup of Sulfolobus cells (right). Going beyond acidic: Extreme acidophiles Some of the most acid-tolerant microorganisms known are archaea, many of which are also thermophilic. Extremely hot and acidic environments are some of the most difficult to get to and sample from, which explains why so few micro organisms from these environments have been isolated. Here are some examples of extreme acidophiles: »» Thermoplasma lacks a cell wall and can live by sulfur respiration in coal refuse piles at temperatures around 55°C and hot springs. CHAPTER 12 Meet the Prokaryotes 191
»» Ferroplasma also has no cell wall but lives in very acidic mine drainage at medium temperatures. It breaks down the pyrite in the mine waste, which acidifies its environment down to a pH of 0. »» Picrophilus is so well adapted to acidity that it can live at a pH of 0 and lower but falls apart when the pH goes up to around 4. Picrophilus has been found in acid mine drainage and active volcanoes. Super salty: Extreme halophiles The haloarchaea, also known as the halobacteria, are extreme halophiles that need extra-salty conditions to live. Often archaeal species will have bacteria in their names. This is a remnant from a time before we knew how very different the domain Archaea is from the domain Bacteria. The level of salt required is sometimes close the maximum amount of salt that water can hold (32 percent), compared to seawater, which contains only about 2.5 percent salt. Most halophiles are strict aerobes, requiring oxygen and get energy from organic matter. Salty environments include brine ponds used to evaporate water from briny solu- tions and salterns, which are areas filled with sea water that are left to evaporate to make sea salt. Naturally salty environments include the pools in Death Valley, the Dead Sea, and soda lakes. Soda lakes are not only super saline but also have a very high pH (alkaline). Here are a few interesting Haloarchaea and halo alkaliphiles (salt and alkaline loving) from soda lakes: »» Halobacteria was the first salt-loving archaeon studied and is the poster child for the group. It was used to learn most of what we know about the cellular structure and adaptations of highly salt-tolerant archaea. Halobacteria have a cell wall made of glycoprotein that is stabilized by the sodium ions (Na+) in the environment. »» Haloquadratum lives in salterns and was named for its unusually shaped square cells, which are thin and filled with gas pockets that let it float to the surface where the oxygen is. »» Natronococcus is a halo alkaliphile found in soda lakes with a pH of between 10 and 12. 192 PART 4 Meeting the Microbes
Some have regular shapes like rods and cocci, whereas others can have very unex- pected shapes like squares or cup-shaped disks. Because water has a tendency to move from an area of low solute concentration to an area of high solute concentration (which is the concept of osmosis), cells have to maintain a higher ion concentration inside than the environmental ion concen- tration. This accumulation of compatible solutes inside the cell is the only thing that stops it from losing water to the hypersaline environment. Halobacterium accumulates massive amounts of potassium (K+) inside its cytoplasm to counter- act the ultra-high concentration of Na+ outside the cell. These microorganisms are so well adapted to their super-salty environments that they can’t live without very high levels of sodium in the environment. Sodium stabilizes the outside of the cells. In addition, they need a large supply of potas- sium, which is required for the proteins and other components inside the cell. Not terribly extreme Archaea Despite making up much less of the known microbial world, archaea have a big impact on the earth’s geochemical cycles. For instance, many primary producers in aquatic and terrestrial habitats are archaea that contribute the carbon cycling in these places. The ammonia oxidizing archaea are another example that are impor- tant players in the nitrogen cycling in the oceans because they’re part of the nitri- fication process. Methanogenic archaea are those that produce methane and live in environments lacking oxygen, such as the digestive tracts of animals (and humans), aquatic sediments, and sewage sludge digesters. They’re important members of carbon cycling, catalyzing the final step in the breakdown of organic matter. Examples include »» Methanobacterium, the cell wall of which contains chondroitin-type material. Chondroitin is a major component of cartilage. »» Methanobrevibacter »» Methanosarcina »» Nitrosopumilus, the ammonia-oxidizing ocean archaea There are archaea living in nonextreme environments, both aquatic and terres- trial, including under polar ice in the Arctic Ocean. Scientists have evidence that they’re there, but none have either been grown in laboratory culture or been fully described. CHAPTER 12 Meet the Prokaryotes 193